User: Ting-Yuan Liu FHCRC

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Posts by Ting-Yuan Liu FHCRC

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Answer: A: Problem with metadata
... Hi Claudia, Here are my suggestions for you: (1) upgrate your R to 2.2.1. You may also want to upgrate it to 2.3.0 again after it releases. R 2.1.1 is a very old version. (2) If you are using R 2.2.1, you could use source("http://bioconductor.org/biocLite.R") biocLite("hgu95a") in R to instal ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Comment: C: AFFX-BioB-3_at annotation
... On Wed, 5 Apr 2006, Wu, Xiwei wrote: > Apparently, I am using the stable release BIOC1.7 annotation packages. > It seems that the problem is fixed in the developmental packages. Why > this probeset is not found in the developmental mouse430a2? It should be > there on the chip. It seem ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Answer: A: AFFX-BioB-3_at annotation
... Hi Xiwei, Could you give us more detail about this? I cannot reproduce your result: > library(hgu133plus2) > get("AFFX-BioB-3_at", hgu133plus2ACCNUM) [1] "AFFX-BIOB-3" > get("AFFX-BioB-3_at", hgu133plus2UNIGENE) [1] NA > library(mouse4302) > get("AFFX-BioB-3_at", mouse4302UNIGENE) ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Answer: A: AnnBuilder package and URLs
... Hi Tabare, Did you set the argument "fromWeb=FALSE"? BTW, could you provide (1) the script you used to build annotation packages, and (2) the output of sessionInfo() so that we could have more ideas about what's going on in your process? Thanks, Ting-Yuan ______________________________________ T ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Comment: C: AnnBuilder
... Hi Hua, On Wed, 29 Mar 2006, Hua Weng wrote: > Hi Ting-Yuan: > > As you suggested, I tried to use "live link" and get files through the web. > First I set source URL like this: > mySrcUrls <- c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA", > UG="ftp://ftp.ncbi.nih.gov/repository/Uni ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Comment: C: AnnBuilder
... Hi Hua, On Tue, 28 Mar 2006, Hua Weng wrote: > My questions are: > 1)If I provide more local annotation files, may I get more information back? Using more annotation files (basefiles) could improves the mapping results, but not the number of environments. It is always a good idea to provi ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Comment: C: AnnBuilder
... Hi Hua, The "subscript out of bounds" bug had been fixed in the developmental AnnBuilder, I believe. Please have a try. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center S ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Answer: A: C. elegans annotation
... Hi Jeff, You mean the annotation package for the Affymetrix C. elegans Genome Array? It will be available in the next release. Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Answer: A: Build an Annotation with GO2ALLPROBES
... Hi Ross, Try myBaseType="gbNRef" HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Fri, 24 Mar 2006 ross.chapman ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780
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Answer: A: AnnBuilder
... Hi Hua, Yes, you could run AnnBuilder in Windows system. That is not what I usually do, but I tried and succeed. However, my R in the windows machine is "built from source" (see section 3.1 of the manual "R Installation and Administration") and it might be a little different from your R (which i ...
written 13.7 years ago by Ting-Yuan Liu FHCRC780

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